Dear all, Starting with today’s preview version of 3D Slicer (r31579), SlicerMorph extension has two ALPACA modules: the regular *ALPACA* and *ALPACA_Preview*.
The preview version uses an ITK-based point cloud registration implementation that we have worked with the Kitware engineers to replace the open3d (O3D) based we currently use. The deformable registration framework based on coherent point drift algorithm (CPD) remains the same in both modules. This change was necessitated by the rapid changes in the O3D API that wasn’t backward compatible and at some point broke our functionality almost on monthly basis, which further exacerbated by the decision of O3D developers not to maintain the older python wheels we relied on. We were concerned about the long-term support of ALPACA and made the decision to have more stable implementation that is entirely based on ITK, which is now available as part of ITK release 5.3. ( https://github.com/InsightSoftwareConsortium/ITK/releases). >From user point of nothing has changed, both modules have exactly the same appearance and functionality. In terms of performance ITK based ALPACA is on-par and in fact slightly better than O3D-based one (as measured by the lower RMSEs). However, ultimately these are two different implementations and there exists a systematic bias in the results based on whether a 3D model is landmarked by O3D or ITK based ALPACA. This has no bearing on the downstream morphometric analyses if your entire dataset is landmarked with one method, but we advise not to mix samples that were landmarked with different modules. This is particularly true, if you are going to use PCA or other decomposition methods which can be sensitive to such systematic differences. Starting with next stable release of 3D Slicer (in the next few months), current ALPACA module will be replaced by the itk based one (ALPACA_preview) and there will be only one ALPACA module. If you are an ALPACA user, interim we suggest you download a preview of 3D Slicer, give the new module a try. We have tried to adjust default parameters of ITK-based one to give similar results to current implementation, but we advise our users to test this with their datasets. ALPACA_preview module is accessible only after you *enable the developer mode in Slicer *(Edit->Application Settings->Developer) and check the “*testing*” option in the module finder (hit CTRL+F, and search for ALPACA). O3D-based current ALPACA implementation will be available in perpetuity as part of the extension catalog of the current Slicer stable version (v5.2.1), but new changes to ALPACA (or other SlicerMorph modules) will not be available to v5.2.1 once the new stable is released. We will discuss these changes in more detail and present results from our analyses during our monthly SlicerMorph user group meeting. If you have questions/concerns please consider attending. Next meeting is at *2/28 11:00 (Seattle Time).* Meeting link is https://seattlechildrens.webex.com/wbxmjs/joinservice/sites/seattlechildrens/meeting/download/812e850e917f40d9afd74ce3a9cdf884?siteurl=seattlechildrens&MTID=me662604e1ffd9c40f25888d048fcc0de. M -- You received this message because you are subscribed to the Google Groups "Morphmet" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/morphmet2/b1418496-4528-49fe-b7c9-cd4657b24a4dn%40googlegroups.com.
